[gmx-users] pdb2gmx error
Dries Van Rompaey
dries.vanrompaey at gmail.com
Wed Oct 7 21:01:32 CEST 2015
This is Gromacs 5.0.4. This is a non-terminal residue.
The command line used is:
gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh)
I tried this procedure with and without ignh flag.
As far as I know, specbonds is not in play.
On 7 October 2015 at 20:56, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> Is it terminal? Are there specbonds in play? What's the GROMACS version?
> What's your pdb2gmx command line? :-)
> On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey <
> dries.vanrompaey at gmail.com>
> > Hi everyone,
> > I'm getting the following warning when I try to run pdb2gmx on my protein
> > structure:
> > WARNING: WARNING: Residue 168 named PRO of a molecule in the input file
> > mapped to an entry in the topology database, but the atom H used in an
> > interaction of type dihedral in that entry is not found in the input
> > Perhaps your atom and/or residue naming needs to be fixed.
> > This warning is only present when I use the AMBER03 forcefield, all other
> > forcefields seem to work fine. I have tried this with both a structure
> > without hydrogens as well as a structure with hydrogens added, both with
> > and without the -ignh flag. I tried looking at the amber03 database files
> > as well as the amber99sb-ildn database files (amber99sb-ildn works just
> > fine), but I could not find any reason why this particular residue would
> > problematic. pdb2gmx does not find any problems with the other proline
> > residues in the protein (which look identical), so I am puzzled as to
> > what's causing this.
> > The proline residue is:
> > ATOM 1384 N PRO A 168 274.650 45.241 24.167 1.00180.63
> > N
> > ATOM 1385 CA PRO A 168 273.508 44.823 23.370 1.00180.63
> > C
> > ATOM 1386 CD PRO A 168 275.844 45.381 23.346 1.00180.63
> > C
> > ATOM 1387 CB PRO A 168 274.071 44.405 22.014 1.00180.63
> > C
> > ATOM 1388 CG PRO A 168 275.381 45.194 21.892 1.00180.63
> > C
> > ATOM 1389 C PRO A 168 272.551 43.776 23.888 1.00180.63
> > C
> > ATOM 1390 O PRO A 168 271.478 43.646 23.304 1.00180.63
> > O
> > Does anyone know what's going on here?
> > Thanks in advance!
> > --
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